[Bug 1903974] Re: issue reading netcdf4 files with nfs v3 on ubuntu 20.04

[Balagopal Pillai]

Thanks Rafael! Disabling hdf5 file locking solved it.

 export HDF5_USE_FILE_LOCKING=FALSE
 
 I didn't have to do this for v3 mounts before. The only time I remember of users having to use this is when using xarray and dask to open the netcdf file in parallel. Anyhow I am happy that it works now. Thanks a lot for your help. Please see the results below - 


export HDF5_USE_FILE_LOCKING=TRUE
ncdump  -h -s MERRA2.19800101.A1.05x0625.NA.nc4 |tail -2
ncdump: MERRA2.19800101.A1.05x0625.NA.nc4: MERRA2.19800101.A1.05x0625.NA.nc4: NetCDF: HDF error

export HDF5_USE_FILE_LOCKING=FALSE
ncdump  -h -s MERRA2.19800101.A1.05x0625.NA.nc4 |tail -2
		:_Format = "netCDF-4"

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https://bugs.launchpad.net/bugs/1903974

Title:
  issue reading netcdf4 files with nfs v3 on ubuntu 20.04

Status in nfs-utils package in Ubuntu:
  New

Bug description:
  I was upgrading a small 16.04 hpc cluster to 20.04 and noticed the
  following. An nfs v3 mount causes netcdf4 file reads to fail. Nfs v4
  mounts from the nfs server running 20.04 works fine. Netcdf3 files
  work fine with both nfs v3 and v4 mounts. I checked a 16.04 setup and
  18.04 setup and they have no issues reading netcdf4 files with nfs v3
  mounts.

       To reproduce this issue, please try any netcdf4 file and try to read the headers like this - 
  ncdump -s -h <filename.nc>. I needed v3 mounts, as I am using posix acls with zfs on the nfs server. So this is an issue particular to nfs server on 20.04 and I would have to move to 18.04 and stay there for a lots of other 16.04 servers and clusters till a solution is found to this issue. Thanks.

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